According to the USDA, the organic industry is the fastest growing segment of U.S. agriculture, with sales rising from $1 billion in 1990 to a projected $23.9 billion in 2009. As of 2006, approximately 20 farms in Alabama were certified organic, in the process of becoming certified, or certified with an alternative label from Certified Naturally Grown, Inc., a non-profit group whose certification is based on USDA organic standards. Organic farms use compost and manure to nourish the soil, rotate crops to avoid nutrient depletion and reduce pest infestation and avoid synthetic fertilizers and pesticides.

Three research units in the Alabama Agricultural Experiment Station system have certified organic research plots and focus on applied research to support small-scale organic farmers.  E.V. Smith Research Center Horticulture Unit is a certified organic vegetable production area while research at the North Alabama Horticulture Research Center is focused on no-till production of tomatoes and peppers in organic systems. The Plant Science Research Center on the Auburn University campus also conducts research in organic production.